Hi All, I have attached the three different datasets for Rn6 genome (rat) and I needed to use circos plot by *circlize package in R*. Please anyone help me in writing the code and making the plot. Any help will be highly appreciated. The three file links are below: File 1: YOUNGCONTROL.csv ( https://drive.google.com/open?id=1arQqlzkRJybclikAByB9w9TCnvmD_Y46 ) File 2: YOUNGTREATED.csv ( https://drive.google.com/open?id=1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO ) File 3: YOUNGTREATED.vs.YOUNGCONTROL.sig.csv ( https://drive.google.com/open?id=0B33BGsdd5x_dOGF0X3BuaWRoMmdSYklOZnJoX09uaWdnNEdN ) The circos plot having the outermost ring contain Rn6 ideogram followed by YOUNGCONTROL, YOUNGTREATED & last innermost circle will be of YOUNGTREATED.vs.YOUNGCONTROL.sig Thanks, Puja
Problems in writing code for circos plot
4 messages · pooja sinha, Jim Lemon, Rolf Turner +1 more
Hi Puja, Three things: 1) Your data files are very large. If you do manage to get circular plots out of them with the circlize library they will probably be very dense. 2) The structure of your data includes too many levels in "Chrom" to get the circlize functions to work. I had to pare them back to the non-random levels. 3) You should probably change the subject line of your message to "Would anyone care to do my work for me?" Jim
On Mon, Jan 27, 2020 at 6:47 AM pooja sinha <pjsinha07 at gmail.com> wrote:
Hi All, I have attached the three different datasets for Rn6 genome (rat) and I needed to use circos plot by *circlize package in R*. Please anyone help me in writing the code and making the plot. Any help will be highly appreciated. The three file links are below: File 1: YOUNGCONTROL.csv ( https://drive.google.com/open?id=1arQqlzkRJybclikAByB9w9TCnvmD_Y46 ) File 2: YOUNGTREATED.csv ( https://drive.google.com/open?id=1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO ) File 3: YOUNGTREATED.vs.YOUNGCONTROL.sig.csv ( https://drive.google.com/open?id=0B33BGsdd5x_dOGF0X3BuaWRoMmdSYklOZnJoX09uaWdnNEdN ) The circos plot having the outermost ring contain Rn6 ideogram followed by YOUNGCONTROL, YOUNGTREATED & last innermost circle will be of YOUNGTREATED.vs.YOUNGCONTROL.sig Thanks, Puja [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
On 27/01/20 11:06 am, Jim Lemon wrote:
Hi Puja, Three things:
<SNIP>
3) You should probably change the subject line of your message to "Would anyone care to do my work for me?"
Fortune nomination!!! :-) cheers, Rolf
Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
Second. Bert
On Sun, Jan 26, 2020 at 2:20 PM Rolf Turner <r.turner at auckland.ac.nz> wrote:
On 27/01/20 11:06 am, Jim Lemon wrote:
Hi Puja, Three things:
<SNIP>
3) You should probably change the subject line of your message to "Would anyone care to do my work for me?"
Fortune nomination!!! :-) cheers, Rolf -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.